The Makassar Strait located between Kalimantan Island to the west and Sulawesi Island to the east, serves as a vital conduit linking the Sulawesi Sea in the north with the Java and Flores Seas in the south. This strait is influenced by material inputs from the Mahakam River and fresh water masses from the Java Sea during boreal winter30. The Makassar Strait also acts as a crucial channel for water masses flowing from the Pacific to the Indian Ocean, where the Labani Channel’s narrow and deep structure generates strong currents and tidal mixing, significantly modifying the ITF in the upper layers19. Stations 48 and 50, situated in proximity to the Sulawesi Sea and the northern Pacific Ocean, exemplify the dynamic interactions between water masses in these areas. Based on water mass conditions, only the layer above 200 m in the Makassar Strait connects to the Lombok Strait, though its characteristics have significantly altered due to internal wave activity31. The Makassar Strait’s vertical water mass structure comprises three layers: surface water above the thermocline, North Pacific Subtropical Water (NPSW) at the thermocline, and North Pacific Intermediate Water (NPIW) in the deep layer32. At Stations 48 and 50, the surface water layer extends to a depth of 110 m. The NPSW characterized by maximum salinity, occupies the 110–220 m range, with its salinity peaking between 110 and 130 m. The NPIW identified by its minimum salinity, was found between 220 and 513 m, with the lowest salinity recorded at 289 m. Beyond 513 m, the deep water predominates characterized by a more uniform temperature and salinity profile, as well as reduced variability in other oceanographic parameters (Fig. 6a–c).Fig. 6(a) Temperature and Salinity (TS) diagram, and (b) Vertical profile of Dissolve Oxygen, (c) Vertical profile of chlorophyll-a.The Lombok Strait located between Bali and Lombok Islands, channels 20–25% of the total ITF water mass from the Makassar Strait31,33. At station 33, salinity was higher and the NPSW signature from the Makassar Strait was absent. A high-salinity layer at 131–156 m, coinciding with low oxygen concentrations, indicates origins from the Northern Indian Ocean (Arabian Sea Water/ASW)34. The lowest salinity layer, found around 260 m, corresponds to Indonesian Upper Water, while a second high-salinity layer at approximately 300 m suggests origins from the Central Indian Ocean. Dissolved oxygen profiles in the Makassar and Lombok Straits were similar, with oxygen-rich upper layers decreasing with depth (Fig. 6b). Therefore, based on the oceanography analysis, the summary is that the water mass at a depth of 1000 m in the Makassar Strait is not connected with the water mass at the same depth in the Lombok Strait and is subject to significantly different oceanographic dynamics.Despite distinct water mass characteristics due to differing bathymetry (Fig. 1b) and dynamics, environmental parameters measured at 1000 m depth in the Makassar Strait and the Lombok Strait exhibit notable stability, as evidenced by consistent profiles of temperature, salinity, pH, chlorophyll-a, nitrate, phosphate and dissolved oxygen (suppl. Table 2). This stability likely plays a significant role in influencing the deep-sea bacterial communities at this depth. Analysis of bacterial diversity across three distinct stations at this depth reveals high diversity, with diversity index values remaining relatively consistent among the stations. This consistency in bacterial diversity is indirectly related to the environmental conditions of the deep-sea water column, which are conducive to microbial life. Bacterial community at 1000 m depth rely on organic matter and nutrient inputs from the surface layers35. The fertility of the surface layers, modulated by processes such as upwelling, mixing, and riverine inputs, impacts the availability of essential materials for deeper layers, thus sustaining microbial life in the deep-sea35,36.The bacterial communities observed at the three stations share significant similarities. Proteobacteria dominate across all stations (33, 48, 50), followed by Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. This is consistent with previous studies showing dominance of Gammaproteobacteria and Alphaproteobacteria in deep-sea waters near the Ninetyeast Ridge in the Indian Ocean37. These findings also align with reports from the Arctic and Pacific Oceans, which highlight Proteobacteria as prevalent38. The presence of genera such as Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter across all stations suggests these deep-sea bacterial genera are well-adapted to high salinity, low temperature, and high hydrostatic pressure.According to the analysis of the specific bacterial species at Station 33(Suppl. Figure 2a), Colwellia psychrerythraea and Photobacterium frigidiphilum were more dominant than the other species. Colwellia psychrerythraea is a marine psychrophilic bacterium that is adaptable to cold conditions. Strains of Colwellia psychrerythraea have been shown to adapt to local deep-sea environments39. Photobacterium frigidiphilum, a gram-negative, Psychrophilic bacterium, was isolated from deep-sea sediments in the western Pacific Ocean40. Candidatus Pelagibacter ubique, an Alphaproteobacteria, was identified at Stations 33, 48, and 50 (Suppl. Figure 2b). This bacterium is known for its ability to thrive in low-nutrient conditions41. The genus Moritella dominated stations 33, and 50 (Suppl. Figure 2a,c), with Moritella marina being one of the most commonly isolated psychrophilic organisms from marine environments. Moritella abyssi was characterized as a gram-negative, non-spore-forming, strictly psychrophilic bacterium42.At the Stations 48 and 50, the Halomonas genus predominated (Suppl. Figure 2b,c). Some of the species found included Halomonas axialensis, Halomonas aquamarine, and Halomonas meridiana. Halomonas axialensis is psychrotolerant and piezotolerant and has the capacity to grow under cold, deep-sea conditions43. Halomonas aquamarine is a slightly halophilic bacterium found in deep-sea sediments at significant depths44,45. Halomonas meridiana is a gram-negative halophilic organism isolated from the Red Sea and recognized for its active L-glutaminase production46. Additionally, the genera Alteromonas and Psychrobacter also exhibited dominance. Alteromonas macleodii is a gram-negative, aerobic marine bacterium found throughout various oceanic environments. It inhabits waters from temperate to tropical zones, encompassing both coastal and pelagic regions47. Psychrobacter pacificensis is a deep-sea psychrophile capable of growing in the absence of NaCl, particularly within deep seawater layers48.This study provides a significant contribution to our understanding of deep-sea bacterial biodiversity within the 1000 m water column along the Indonesian Throughflow (ITF) route, specifically in the Makassar and Lombok Straits. The findings reveal a high level of biodiversity, reflecting the complexity of the deep-sea ecosystem in these regions. This ecosystem is characterized by extreme environmental conditions, including low temperatures, low oxygen levels, elevated pH, high salinity, and intense hydrostatic pressure, which collectively create a habitat for a highly specialized and exclusive bacterial community. To the best of our knowledge, this study is the first to document the presence of Colwellia psychrerythraea, Moritella marina, Halomonas meridiana, Photobacterium frigidiphilum, Candidatus Pelagibacter, Alteromonas macleodii, and Psychrobacter pacificensis in the deep-sea waters of Indonesia, specifically within the 1000-m water column, using 16S rRNA gene. Building on these findings, future research should explore the ecological roles and metabolic pathways of these microorganisms, as well as their interactions within the tropical deep-sea ecosystem. Additionally, bioprospecting could uncover novel enzymes, bioactive compounds, or metabolites with applications in biotechnology, medicine, and industry.
